Explicyte is proud to be a certified Nanostring partner - Let’s start the Digital Spatial Profiling revolution together
12 / 08 / 2019
To deal with this level of complexity, it’s therefore critical to benefit from technological platform allowing for specific investigation in compartments of interest (eg. tumor vs stroma). Thanks to the GeoMx® platform (Nanostring Inc.), which combines the spatial resolution of immunohistofluorescence with the high-plex gene/protein expression analysis, the Digital Spatial Profiling (DSP) revolution has started.
Digital spatial profiling of human lung adenocarcinomas through Cancer Transcriptome Atlas
A) FFPE tissue section from human lung cancer was stained with a cocktail of standard fluorescent morphology markers (i.e. PanCK in red, CD45 in green) and counterstained with Sytox (Nuclei staining) as to allow tissue segmentation. Concomitantly with the morphology markers, oligo-tagged ISH probes (RNA) targeting 1,800 genes from the CTA were applied. Regions of interest (ROI) were then selected and segmented into Stroma and Tumor areas thanks to the morphology markers. Oligos from selected areas (Areas of Illumination, AOIs) were released upon exposure to UV light and collected via a microcapillary tube and processed for library preparation and next generation sequencing.
(B) Heatmap view of the unsupervised clustering of 15 ROIs (divided in 15 AOIs in stroma and 15 AOIs in tumor) according to the 1,800 genes expression profile. In the heatmap, the Y-axis represents the 1,800 genes and the X-axis represents the AOIs. The expression levels from low to high are represented as a color gradient from blue to red, respectively.
(C) Volcano plot representation of differential gene expression between stroma and tumor areas collected from the different ROIs. Vertical dotted lines represent ± Log2(FC>2) while the horizontal dotted line indicates a p-value of 0,05. Genes highlighted in red on the left part of the volcano plot are those significantly enriched in the tumor compartment (eg. CK19) while on the right part, genes significantly enriched in the stroma are depicted.